neighbors graph not updating correctly?

[drbergman]

It seems that the neighbors graph might not be updating correctly. I'm extending @vincent-noel's (I think? Or maybe @rheiland's) spring attachment viewer in studio to include neighbors and old school attachments. Also to overlay it onto the svg. Looks like in this simulation some cells in the bottom-right are labeled as neighbors despite not being overlapping (which is how they are defined in the cpp).

[drbergman]

[rheiland]

Was a terrific @vincent-noel contribution - which I've been using a lot lately for spring attachments (and has me thinking there's yet another, entirely different bug, unrelated to the "links" plots).
The Zen in me wants to say: the neighbor of my neighbor is my neighbor.
Is it possible you didn't take into account the "relative max adhesion distance"?

[rheiland]

using these 3 pts:
x,y,z,type,volume,cycle entry,custom:GFP,custom:sample
0.0,0.0,0.0,default
9.0,9.0,0.0,default
-9.,9.0,0.0,default

• with default "relative max adhesion distance" = 1.25
  output_test_tri/output00000001_cell_neighbor_graph.txt
  0: 1,2
  1: 0,2
  2: 0,1

• with "relative max adhesion distance" = 1.
  0: 1,2
  1: 0
  2: 0

[vincent-noel]

Thanks for looking into this @drbergman ! Especially the display on SVGs was clearly lacking.
I coded this quickly for one project, and felt like I never tested enough. So there might be bugs indeed.

I was also never sure when the old school atachments were used, or if it was dead code (I remember only one sample project using it). And for sure it's useful for neighbours !